Restricted and degraded habitat is the greatest threat to giant pandas. Population fragmentation exists on two scales — six mountain ranges separated by agriculture, and within these, fragments of bamboo forest separated by patches of cleared lands and forest without a bamboo understory. The giant panda's range contracted as trees were removed in logging operations and land was cleared for farming. Populations of pandas thereby became small and isolated, and confined to high ridges, hemmed in by cultivation.

Chinese authorities have established a network of panda reserves, and linkages now exist among some of these, but small population size and small total range remains a threat to the viability of this species. Moreover, in some reserves, and especially in panda range outside reserves, habitat has become degraded by intensive human use (Liu et al. 2001).

A further threat to pandas relates to their reliance on bamboo for food. Bamboo is subject to periodic, synchronous (and hence large-scale) flowering and die-off (at intervals of 15–120 years). Before significant human encroachment of their habitat, pandas could move to areas with healthy bamboo when a die-off occurred. Studies following the latest major bamboo die-off in the early 1980s indicated that pandas were still able to survive by finding patches that had not flowered, and also by moving to alternate habitats and feeding on less-favoured species of bamboo (Johnson et al. 1988, Reid et al. 1989).

Poaching of pandas was a serious problem in the past, but it has greatly diminished, and is no longer considered a major threat. Markets for panda skins have virtually disappeared, and penalties for poaching pandas have become far more severe (including death sentences in some cases). Panda parts are not used in Traditional Chinese Medicine. However, giant pandas are still sometimes killed in snares set for musk deer and other species.